Understanding the relationship between genotype and phenotype is essential to use genomic information for personalized or predictive medicine. The long-term goal of our work is to understand mechanisms that generate phenotypic variation in order to advance our understanding of structural birth defects of the craniofacial complex. Morphogenesis is an emergent property of development that makes the relationship between genotype and phenotype complex. In this application we will expand on work that we performed during our first round of funding, and we will broaden the scope of our work to generate a more global understanding of genotype-phenotype relationship during morphogenesis of the face. Previously, we demonstrated that a non-linear relationship between Sonic hedgehog (Shh) signaling and facial shape variation exists, whereby small changes in SHH signaling produce large phenotypic changes. Our preliminary data suggests that this is a fundamental property of signaling systems. In addition, we have determined that the shape of gene expression domains is highly associated with changes in morphology, and that there is genetic variation in the propensity to exhibit a range of phenotypic outcomes for a particular genotype. These preliminary data have led us to the hypothesis that variation in facial morphology emerges, in part, from molecular signaling mechanisms that modulate, not only signal magnitude, but also signal variation and the spatial organization of signaling centers. We will test this hypothesis in three Aims. First, we will use the Fgf8 allelic series of mice to generate phenotypic variation based on levels of FGF8 signaling and we will relate phenotypic outcomes with levels of pathway activity and cellular behaviors. Second, we will alter the shape of the Frontonasal Ectodermal Zone (FEZ) in the avian face, because the FEZ regulates morphogenesis of the upper jaw. We will then directly relate the shape of the FEZ to molecular, cellular, and morphological outcomes. Third, we will test genomic-level implications of the mechanisms investigated in aims 1 and 2 in a large group of recombinant inbred mouse strains. In this aim, we test the genetic basis for the modulation of phenotypic variance and we explore the genomic implications of the hypothesis that the genetics of morphology is less additive than is commonly assumed. Non-additive genetic variation is a major challenge to current genomic approaches to complex traits. We believe that the results of our work will make a significant contribution to understanding the relationship between genotype and phenotype in the production structural diseases of the craniofacial complex.